[7735] | 1 | """ Classes to read an SWW file. |
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| 2 | """ |
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| 3 | |
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| 4 | from anuga.coordinate_transforms.geo_reference import Geo_reference |
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| 5 | from anuga.config import netcdf_mode_r, netcdf_mode_w, netcdf_mode_a |
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| 6 | from anuga.config import netcdf_float, netcdf_float32, netcdf_int |
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| 7 | from anuga.config import max_float |
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| 8 | from anuga.utilities.numerical_tools import ensure_numeric |
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[7742] | 9 | import anuga.utilities.log as log |
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[7735] | 10 | from Scientific.IO.NetCDF import NetCDFFile |
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| 11 | |
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[7858] | 12 | from sts import Write_sts |
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| 13 | |
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[7735] | 14 | from anuga.coordinate_transforms.geo_reference import \ |
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| 15 | ensure_geo_reference |
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| 16 | |
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| 17 | from file_utils import create_filename |
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| 18 | import numpy as num |
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| 19 | |
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| 20 | ## |
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| 21 | # @brief Generic class for storing output to e.g. visualisation or checkpointing |
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| 22 | class Data_format: |
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| 23 | """Generic interface to data formats |
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| 24 | """ |
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| 25 | |
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| 26 | ## |
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| 27 | # @brief Instantiate this instance. |
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| 28 | # @param domain |
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| 29 | # @param extension |
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| 30 | # @param mode The mode of the underlying file. |
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| 31 | def __init__(self, domain, extension, mode=netcdf_mode_w): |
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| 32 | assert mode[0] in ['r', 'w', 'a'], \ |
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| 33 | "Mode %s must be either:\n" % mode + \ |
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| 34 | " 'w' (write)\n" + \ |
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| 35 | " 'r' (read)\n" + \ |
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| 36 | " 'a' (append)" |
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| 37 | |
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| 38 | #Create filename |
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| 39 | self.filename = create_filename(domain.get_datadir(), |
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| 40 | domain.get_name(), extension) |
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| 41 | |
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| 42 | self.timestep = 0 |
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| 43 | self.domain = domain |
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| 44 | |
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| 45 | # Exclude ghosts in case this is a parallel domain |
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| 46 | self.number_of_nodes = domain.number_of_full_nodes |
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| 47 | self.number_of_volumes = domain.number_of_full_triangles |
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| 48 | #self.number_of_volumes = len(domain) |
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| 49 | |
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| 50 | #FIXME: Should we have a general set_precision function? |
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| 51 | |
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| 52 | |
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| 53 | class SWW_file(Data_format): |
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| 54 | """Interface to native NetCDF format (.sww) for storing model output |
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| 55 | |
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| 56 | There are two kinds of data |
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| 57 | |
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| 58 | 1: Constant data: Vertex coordinates and field values. Stored once |
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| 59 | 2: Variable data: Conserved quantities. Stored once per timestep. |
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| 60 | |
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| 61 | All data is assumed to reside at vertex locations. |
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| 62 | """ |
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| 63 | |
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| 64 | ## |
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| 65 | # @brief Instantiate this instance. |
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| 66 | # @param domain ?? |
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| 67 | # @param mode Mode of the underlying data file. |
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| 68 | # @param max_size ?? |
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| 69 | # @param recursion ?? |
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| 70 | # @note Prepare the underlying data file if mode starts with 'w'. |
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| 71 | def __init__(self, domain, |
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| 72 | mode=netcdf_mode_w, max_size=2000000000, recursion=False): |
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| 73 | from Scientific.IO.NetCDF import NetCDFFile |
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| 74 | |
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| 75 | self.precision = netcdf_float32 # Use single precision for quantities |
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| 76 | self.recursion = recursion |
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| 77 | self.mode = mode |
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| 78 | if hasattr(domain, 'max_size'): |
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| 79 | self.max_size = domain.max_size # File size max is 2Gig |
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| 80 | else: |
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| 81 | self.max_size = max_size |
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| 82 | if hasattr(domain, 'minimum_storable_height'): |
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| 83 | self.minimum_storable_height = domain.minimum_storable_height |
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| 84 | else: |
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| 85 | self.minimum_storable_height = default_minimum_storable_height |
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| 86 | |
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| 87 | # Call parent constructor |
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| 88 | Data_format.__init__(self, domain, 'sww', mode) |
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| 89 | |
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| 90 | # Get static and dynamic quantities from domain |
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| 91 | static_quantities = [] |
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| 92 | dynamic_quantities = [] |
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| 93 | |
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| 94 | for q in domain.quantities_to_be_stored: |
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| 95 | flag = domain.quantities_to_be_stored[q] |
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| 96 | |
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| 97 | msg = 'Quantity %s is requested to be stored ' % q |
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| 98 | msg += 'but it does not exist in domain.quantities' |
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| 99 | assert q in domain.quantities, msg |
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| 100 | |
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| 101 | assert flag in [1,2] |
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| 102 | if flag == 1: static_quantities.append(q) |
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| 103 | if flag == 2: dynamic_quantities.append(q) |
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| 104 | |
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| 105 | |
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| 106 | # NetCDF file definition |
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| 107 | fid = NetCDFFile(self.filename, mode) |
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| 108 | if mode[0] == 'w': |
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| 109 | description = 'Output from anuga.abstract_2d_finite_volumes ' \ |
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| 110 | 'suitable for plotting' |
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| 111 | |
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| 112 | self.writer = Write_sww(static_quantities, dynamic_quantities) |
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| 113 | self.writer.store_header(fid, |
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| 114 | domain.starttime, |
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| 115 | self.number_of_volumes, |
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| 116 | self.domain.number_of_full_nodes, |
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| 117 | description=description, |
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| 118 | smoothing=domain.smooth, |
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| 119 | order=domain.default_order, |
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| 120 | sww_precision=self.precision) |
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| 121 | |
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| 122 | # Extra optional information |
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| 123 | if hasattr(domain, 'texture'): |
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| 124 | fid.texture = domain.texture |
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| 125 | |
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| 126 | if domain.quantities_to_be_monitored is not None: |
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| 127 | fid.createDimension('singleton', 1) |
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| 128 | fid.createDimension('two', 2) |
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| 129 | |
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| 130 | poly = domain.monitor_polygon |
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| 131 | if poly is not None: |
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| 132 | N = len(poly) |
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| 133 | fid.createDimension('polygon_length', N) |
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| 134 | fid.createVariable('extrema.polygon', |
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| 135 | self.precision, |
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| 136 | ('polygon_length', 'two')) |
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| 137 | fid.variables['extrema.polygon'][:] = poly |
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| 138 | |
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| 139 | interval = domain.monitor_time_interval |
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| 140 | if interval is not None: |
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| 141 | fid.createVariable('extrema.time_interval', |
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| 142 | self.precision, |
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| 143 | ('two',)) |
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| 144 | fid.variables['extrema.time_interval'][:] = interval |
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| 145 | |
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| 146 | for q in domain.quantities_to_be_monitored: |
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| 147 | fid.createVariable(q + '.extrema', self.precision, |
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| 148 | ('numbers_in_range',)) |
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| 149 | fid.createVariable(q + '.min_location', self.precision, |
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| 150 | ('numbers_in_range',)) |
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| 151 | fid.createVariable(q + '.max_location', self.precision, |
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| 152 | ('numbers_in_range',)) |
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| 153 | fid.createVariable(q + '.min_time', self.precision, |
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| 154 | ('singleton',)) |
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| 155 | fid.createVariable(q + '.max_time', self.precision, |
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| 156 | ('singleton',)) |
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| 157 | |
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| 158 | fid.close() |
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| 159 | |
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| 160 | ## |
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| 161 | # @brief Store connectivity data into the underlying data file. |
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| 162 | def store_connectivity(self): |
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| 163 | """Store information about nodes, triangles and static quantities |
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| 164 | |
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| 165 | Writes x,y coordinates of triangles and their connectivity. |
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| 166 | |
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| 167 | Store also any quantity that has been identified as static. |
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| 168 | """ |
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| 169 | |
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| 170 | # FIXME: Change name to reflect the fact thta this function |
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| 171 | # stores both connectivity (triangulation) and static quantities |
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| 172 | |
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| 173 | from Scientific.IO.NetCDF import NetCDFFile |
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| 174 | |
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| 175 | domain = self.domain |
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| 176 | |
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| 177 | # append to the NetCDF file |
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| 178 | fid = NetCDFFile(self.filename, netcdf_mode_a) |
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| 179 | |
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| 180 | # Get X, Y from one (any) of the quantities |
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| 181 | Q = domain.quantities.values()[0] |
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| 182 | X,Y,_,V = Q.get_vertex_values(xy=True, precision=self.precision) |
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| 183 | |
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| 184 | # store the connectivity data |
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| 185 | points = num.concatenate((X[:,num.newaxis],Y[:,num.newaxis]), axis=1) |
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| 186 | self.writer.store_triangulation(fid, |
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| 187 | points, |
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| 188 | V.astype(num.float32), |
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| 189 | points_georeference=\ |
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| 190 | domain.geo_reference) |
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| 191 | |
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| 192 | |
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| 193 | # Get names of static quantities |
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| 194 | static_quantities = {} |
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| 195 | for name in self.writer.static_quantities: |
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| 196 | Q = domain.quantities[name] |
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| 197 | A, _ = Q.get_vertex_values(xy=False, |
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| 198 | precision=self.precision) |
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| 199 | static_quantities[name] = A |
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| 200 | |
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| 201 | # Store static quantities |
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| 202 | self.writer.store_static_quantities(fid, **static_quantities) |
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| 203 | |
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| 204 | fid.close() |
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| 205 | |
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| 206 | ## |
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| 207 | # @brief Store time and time dependent quantities |
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| 208 | # to the underlying data file. |
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| 209 | def store_timestep(self): |
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| 210 | """Store time and time dependent quantities |
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| 211 | """ |
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| 212 | |
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| 213 | from Scientific.IO.NetCDF import NetCDFFile |
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| 214 | import types |
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| 215 | from time import sleep |
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| 216 | from os import stat |
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| 217 | |
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| 218 | # Get NetCDF |
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| 219 | retries = 0 |
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| 220 | file_open = False |
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| 221 | while not file_open and retries < 10: |
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| 222 | try: |
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| 223 | # Open existing file |
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| 224 | fid = NetCDFFile(self.filename, netcdf_mode_a) |
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| 225 | except IOError: |
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| 226 | # This could happen if someone was reading the file. |
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| 227 | # In that case, wait a while and try again |
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| 228 | msg = 'Warning (store_timestep): File %s could not be opened' \ |
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| 229 | % self.filename |
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| 230 | msg += ' - trying step %s again' % self.domain.time |
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| 231 | log.critical(msg) |
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| 232 | retries += 1 |
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| 233 | sleep(1) |
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| 234 | else: |
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| 235 | file_open = True |
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| 236 | |
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| 237 | if not file_open: |
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| 238 | msg = 'File %s could not be opened for append' % self.filename |
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| 239 | raise DataFileNotOpenError, msg |
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| 240 | |
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| 241 | # Check to see if the file is already too big: |
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| 242 | time = fid.variables['time'] |
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| 243 | i = len(time) + 1 |
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| 244 | file_size = stat(self.filename)[6] |
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| 245 | file_size_increase = file_size / i |
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| 246 | if file_size + file_size_increase > self.max_size * 2**self.recursion: |
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| 247 | # In order to get the file name and start time correct, |
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| 248 | # I change the domain.filename and domain.starttime. |
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| 249 | # This is the only way to do this without changing |
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| 250 | # other modules (I think). |
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| 251 | |
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| 252 | # Write a filename addon that won't break the anuga viewers |
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| 253 | # (10.sww is bad) |
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| 254 | filename_ext = '_time_%s' % self.domain.time |
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| 255 | filename_ext = filename_ext.replace('.', '_') |
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| 256 | |
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| 257 | # Remember the old filename, then give domain a |
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| 258 | # name with the extension |
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| 259 | old_domain_filename = self.domain.get_name() |
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| 260 | if not self.recursion: |
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| 261 | self.domain.set_name(old_domain_filename + filename_ext) |
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| 262 | |
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| 263 | # Temporarily change the domain starttime to the current time |
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| 264 | old_domain_starttime = self.domain.starttime |
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| 265 | self.domain.starttime = self.domain.get_time() |
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| 266 | |
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| 267 | # Build a new data_structure. |
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| 268 | next_data_structure = SWW_file(self.domain, mode=self.mode, |
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| 269 | max_size=self.max_size, |
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| 270 | recursion=self.recursion+1) |
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| 271 | if not self.recursion: |
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| 272 | log.critical(' file_size = %s' % file_size) |
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| 273 | log.critical(' saving file to %s' |
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| 274 | % next_data_structure.filename) |
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| 275 | |
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| 276 | # Set up the new data_structure |
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| 277 | self.domain.writer = next_data_structure |
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| 278 | |
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| 279 | # Store connectivity and first timestep |
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| 280 | next_data_structure.store_connectivity() |
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| 281 | next_data_structure.store_timestep() |
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| 282 | fid.sync() |
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| 283 | fid.close() |
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| 284 | |
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| 285 | # Restore the old starttime and filename |
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| 286 | self.domain.starttime = old_domain_starttime |
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| 287 | self.domain.set_name(old_domain_filename) |
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| 288 | else: |
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| 289 | self.recursion = False |
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| 290 | domain = self.domain |
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| 291 | |
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| 292 | # Get the variables |
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| 293 | time = fid.variables['time'] |
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| 294 | i = len(time) |
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| 295 | |
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| 296 | if 'stage' in self.writer.dynamic_quantities: |
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| 297 | # Select only those values for stage, |
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| 298 | # xmomentum and ymomentum (if stored) where |
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| 299 | # depth exceeds minimum_storable_height |
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| 300 | # |
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| 301 | # In this branch it is assumed that elevation |
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| 302 | # is also available as a quantity |
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| 303 | |
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| 304 | Q = domain.quantities['stage'] |
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| 305 | w, _ = Q.get_vertex_values(xy=False) |
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| 306 | |
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| 307 | Q = domain.quantities['elevation'] |
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| 308 | z, _ = Q.get_vertex_values(xy=False) |
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| 309 | |
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| 310 | storable_indices = (w-z >= self.minimum_storable_height) |
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| 311 | else: |
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| 312 | # Very unlikely branch |
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| 313 | storable_indices = None # This means take all |
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| 314 | |
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| 315 | |
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| 316 | # Now store dynamic quantities |
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| 317 | dynamic_quantities = {} |
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| 318 | for name in self.writer.dynamic_quantities: |
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| 319 | netcdf_array = fid.variables[name] |
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| 320 | |
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| 321 | Q = domain.quantities[name] |
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| 322 | A, _ = Q.get_vertex_values(xy=False, |
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| 323 | precision=self.precision) |
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| 324 | |
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| 325 | if storable_indices is not None: |
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| 326 | if name == 'stage': |
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| 327 | A = num.choose(storable_indices, (z, A)) |
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| 328 | |
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| 329 | if name in ['xmomentum', 'ymomentum']: |
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| 330 | # Get xmomentum where depth exceeds |
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| 331 | # minimum_storable_height |
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| 332 | |
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| 333 | # Define a zero vector of same size and type as A |
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| 334 | # for use with momenta |
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| 335 | null = num.zeros(num.size(A), A.dtype.char) |
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| 336 | A = num.choose(storable_indices, (null, A)) |
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| 337 | |
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| 338 | dynamic_quantities[name] = A |
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| 339 | |
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| 340 | |
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| 341 | # Store dynamic quantities |
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| 342 | self.writer.store_quantities(fid, |
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| 343 | time=self.domain.time, |
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| 344 | sww_precision=self.precision, |
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| 345 | **dynamic_quantities) |
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| 346 | |
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| 347 | |
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| 348 | # Update extrema if requested |
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| 349 | domain = self.domain |
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| 350 | if domain.quantities_to_be_monitored is not None: |
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| 351 | for q, info in domain.quantities_to_be_monitored.items(): |
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| 352 | if info['min'] is not None: |
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| 353 | fid.variables[q + '.extrema'][0] = info['min'] |
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| 354 | fid.variables[q + '.min_location'][:] = \ |
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| 355 | info['min_location'] |
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| 356 | fid.variables[q + '.min_time'][0] = info['min_time'] |
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| 357 | |
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| 358 | if info['max'] is not None: |
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| 359 | fid.variables[q + '.extrema'][1] = info['max'] |
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| 360 | fid.variables[q + '.max_location'][:] = \ |
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| 361 | info['max_location'] |
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| 362 | fid.variables[q + '.max_time'][0] = info['max_time'] |
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| 363 | |
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| 364 | # Flush and close |
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| 365 | fid.sync() |
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| 366 | fid.close() |
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| 367 | |
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| 368 | |
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| 369 | ## |
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| 370 | # @brief Class to open an sww file so that domain can be populated with quantity values |
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| 371 | class Read_sww: |
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| 372 | |
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| 373 | def __init__(self, source): |
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| 374 | """The source parameter is assumed to be a NetCDF sww file. |
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| 375 | """ |
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| 376 | |
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| 377 | self.source = source |
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| 378 | |
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| 379 | self.frame_number = 0 |
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| 380 | |
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| 381 | fin = NetCDFFile(self.source, 'r') |
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| 382 | |
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| 383 | self.time = num.array(fin.variables['time'], num.float) |
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| 384 | self.last_frame_number = self.time.shape[0] - 1 |
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| 385 | |
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| 386 | self.frames = num.arange(self.last_frame_number+1) |
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| 387 | |
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| 388 | fin.close() |
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| 389 | |
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| 390 | self.read_mesh() |
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| 391 | |
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| 392 | self.quantities = {} |
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| 393 | |
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| 394 | self.read_quantities() |
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| 395 | |
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| 396 | |
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| 397 | def read_mesh(self): |
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[7841] | 398 | """ Read and store the mesh data contained within this sww file. |
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| 399 | """ |
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[7735] | 400 | fin = NetCDFFile(self.source, 'r') |
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| 401 | |
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| 402 | self.vertices = num.array(fin.variables['volumes'], num.int) |
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| 403 | |
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| 404 | self.x = x = num.array(fin.variables['x'], num.float) |
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| 405 | self.y = y = num.array(fin.variables['y'], num.float) |
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| 406 | |
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| 407 | assert len(self.x) == len(self.y) |
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| 408 | |
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| 409 | self.xmin = num.min(x) |
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| 410 | self.xmax = num.max(x) |
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| 411 | self.ymin = num.min(y) |
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| 412 | self.ymax = num.max(y) |
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| 413 | |
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| 414 | |
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| 415 | fin.close() |
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| 416 | |
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| 417 | def read_quantities(self, frame_number=0): |
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[7841] | 418 | """ |
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| 419 | Read the quantities contained in this file. |
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| 420 | frame_number is the time index to load. |
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| 421 | """ |
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[7735] | 422 | assert frame_number >= 0 and frame_number <= self.last_frame_number |
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| 423 | |
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| 424 | self.frame_number = frame_number |
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| 425 | |
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| 426 | M = len(self.x)/3 |
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| 427 | |
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| 428 | fin = NetCDFFile(self.source, 'r') |
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| 429 | |
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| 430 | for q in filter(lambda n:n != 'x' and n != 'y' and n != 'time' and n != 'volumes' and \ |
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| 431 | '_range' not in n, \ |
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| 432 | fin.variables.keys()): |
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| 433 | if len(fin.variables[q].shape) == 1: # Not a time-varying quantity |
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| 434 | self.quantities[q] = num.ravel(num.array(fin.variables[q], num.float)).reshape(M,3) |
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| 435 | else: # Time-varying, get the current timestep data |
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| 436 | self.quantities[q] = num.array(fin.variables[q][self.frame_number], num.float).reshape(M,3) |
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| 437 | fin.close() |
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| 438 | return self.quantities |
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| 439 | |
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| 440 | def get_bounds(self): |
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[7841] | 441 | """ |
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| 442 | Get the bounding rect around the mesh. |
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| 443 | """ |
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[7735] | 444 | return [self.xmin, self.xmax, self.ymin, self.ymax] |
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| 445 | |
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| 446 | def get_last_frame_number(self): |
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[7841] | 447 | """ |
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| 448 | Return the last loaded frame index. |
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| 449 | """ |
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[7735] | 450 | return self.last_frame_number |
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| 451 | |
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| 452 | def get_time(self): |
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[7841] | 453 | """ |
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| 454 | Get time at the current frame num, in secs. |
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| 455 | """ |
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[7735] | 456 | return self.time[self.frame_number] |
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| 457 | |
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| 458 | |
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[7858] | 459 | class Write_sww(Write_sts): |
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[7841] | 460 | """ |
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| 461 | A class to write an SWW file. |
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| 462 | |
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| 463 | It is domain agnostic, and requires all the data to be fed in |
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| 464 | manually. |
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| 465 | """ |
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[7735] | 466 | |
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| 467 | def __init__(self, static_quantities, dynamic_quantities): |
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| 468 | """Initialise Write_sww with two list af quantity names: |
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| 469 | |
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| 470 | static_quantities (e.g. elevation or friction): |
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| 471 | Stored once at the beginning of the simulation in a 1D array |
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| 472 | of length number_of_points |
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| 473 | dynamic_quantities (e.g stage): |
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| 474 | Stored every timestep in a 2D array with |
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| 475 | dimensions number_of_points X number_of_timesteps |
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| 476 | |
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| 477 | """ |
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| 478 | self.static_quantities = static_quantities |
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| 479 | self.dynamic_quantities = dynamic_quantities |
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| 480 | |
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| 481 | |
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| 482 | def store_header(self, |
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| 483 | outfile, |
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| 484 | times, |
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| 485 | number_of_volumes, |
---|
| 486 | number_of_points, |
---|
| 487 | description='Generated by ANUGA', |
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| 488 | smoothing=True, |
---|
| 489 | order=1, |
---|
| 490 | sww_precision=netcdf_float32, |
---|
| 491 | verbose=False): |
---|
| 492 | """Write an SWW file header. |
---|
| 493 | |
---|
[7841] | 494 | Writes the first section of the .sww file. |
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| 495 | |
---|
[7735] | 496 | outfile - the open file that will be written |
---|
| 497 | times - A list of the time slice times OR a start time |
---|
| 498 | Note, if a list is given the info will be made relative. |
---|
| 499 | number_of_volumes - the number of triangles |
---|
[7841] | 500 | number_of_points - the number of vertices in the mesh |
---|
[7735] | 501 | """ |
---|
| 502 | |
---|
[7736] | 503 | from anuga.abstract_2d_finite_volumes.util \ |
---|
| 504 | import get_revision_number |
---|
| 505 | |
---|
[7735] | 506 | outfile.institution = 'Geoscience Australia' |
---|
| 507 | outfile.description = description |
---|
| 508 | |
---|
| 509 | # For sww compatibility |
---|
| 510 | if smoothing is True: |
---|
| 511 | # Smoothing to be depreciated |
---|
| 512 | outfile.smoothing = 'Yes' |
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| 513 | outfile.vertices_are_stored_uniquely = 'False' |
---|
| 514 | else: |
---|
| 515 | # Smoothing to be depreciated |
---|
| 516 | outfile.smoothing = 'No' |
---|
| 517 | outfile.vertices_are_stored_uniquely = 'True' |
---|
| 518 | outfile.order = order |
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| 519 | |
---|
| 520 | try: |
---|
| 521 | revision_number = get_revision_number() |
---|
| 522 | except: |
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[7736] | 523 | # This will be triggered if the system cannot get the SVN |
---|
| 524 | # revision number. |
---|
[7735] | 525 | revision_number = None |
---|
| 526 | # Allow None to be stored as a string |
---|
| 527 | outfile.revision_number = str(revision_number) |
---|
| 528 | |
---|
| 529 | # This is being used to seperate one number from a list. |
---|
| 530 | # what it is actually doing is sorting lists from numeric arrays. |
---|
| 531 | if isinstance(times, (list, num.ndarray)): |
---|
| 532 | number_of_times = len(times) |
---|
| 533 | times = ensure_numeric(times) |
---|
| 534 | if number_of_times == 0: |
---|
| 535 | starttime = 0 |
---|
| 536 | else: |
---|
| 537 | starttime = times[0] |
---|
| 538 | times = times - starttime #Store relative times |
---|
| 539 | else: |
---|
| 540 | number_of_times = 0 |
---|
| 541 | starttime = times |
---|
| 542 | |
---|
| 543 | |
---|
| 544 | outfile.starttime = starttime |
---|
| 545 | |
---|
| 546 | # dimension definitions |
---|
| 547 | outfile.createDimension('number_of_volumes', number_of_volumes) |
---|
| 548 | outfile.createDimension('number_of_vertices', 3) |
---|
| 549 | outfile.createDimension('numbers_in_range', 2) |
---|
| 550 | |
---|
| 551 | if smoothing is True: |
---|
| 552 | outfile.createDimension('number_of_points', number_of_points) |
---|
| 553 | # FIXME(Ole): This will cause sww files for parallel domains to |
---|
| 554 | # have ghost nodes stored (but not used by triangles). |
---|
| 555 | # To clean this up, we have to change get_vertex_values and |
---|
| 556 | # friends in quantity.py (but I can't be bothered right now) |
---|
| 557 | else: |
---|
| 558 | outfile.createDimension('number_of_points', 3*number_of_volumes) |
---|
| 559 | |
---|
| 560 | outfile.createDimension('number_of_timesteps', number_of_times) |
---|
| 561 | |
---|
| 562 | # variable definitions |
---|
| 563 | outfile.createVariable('x', sww_precision, ('number_of_points',)) |
---|
| 564 | outfile.createVariable('y', sww_precision, ('number_of_points',)) |
---|
| 565 | |
---|
| 566 | outfile.createVariable('volumes', netcdf_int, ('number_of_volumes', |
---|
| 567 | 'number_of_vertices')) |
---|
| 568 | |
---|
| 569 | |
---|
| 570 | for q in self.static_quantities: |
---|
| 571 | |
---|
| 572 | outfile.createVariable(q, sww_precision, |
---|
| 573 | ('number_of_points',)) |
---|
| 574 | |
---|
| 575 | outfile.createVariable(q + Write_sww.RANGE, sww_precision, |
---|
| 576 | ('numbers_in_range',)) |
---|
| 577 | |
---|
| 578 | # Initialise ranges with small and large sentinels. |
---|
| 579 | # If this was in pure Python we could have used None sensibly |
---|
| 580 | outfile.variables[q+Write_sww.RANGE][0] = max_float # Min |
---|
| 581 | outfile.variables[q+Write_sww.RANGE][1] = -max_float # Max |
---|
| 582 | |
---|
[7858] | 583 | |
---|
| 584 | self.write_dynamic_quantities(outfile, self.dynamic_quantities, times) |
---|
[7735] | 585 | |
---|
| 586 | |
---|
| 587 | |
---|
| 588 | def store_triangulation(self, |
---|
| 589 | outfile, |
---|
| 590 | points_utm, |
---|
| 591 | volumes, |
---|
| 592 | zone=None, |
---|
| 593 | new_origin=None, |
---|
| 594 | points_georeference=None, |
---|
| 595 | verbose=False): |
---|
| 596 | """ |
---|
[7841] | 597 | Store triangulation data in the underlying file. |
---|
| 598 | |
---|
| 599 | Stores the points and triangle indices in the sww file |
---|
| 600 | |
---|
| 601 | outfile Open handle to underlying file. |
---|
| 602 | |
---|
| 603 | new_origin georeference that the points can be set to. |
---|
| 604 | |
---|
| 605 | points_georeference The georeference of the points_utm. |
---|
| 606 | |
---|
| 607 | verbose True if this function is to be verbose. |
---|
| 608 | |
---|
[7735] | 609 | new_origin - qa georeference that the points can be set to. (Maybe |
---|
| 610 | do this before calling this function.) |
---|
| 611 | |
---|
| 612 | points_utm - currently a list or array of the points in UTM. |
---|
| 613 | points_georeference - the georeference of the points_utm |
---|
| 614 | |
---|
| 615 | How about passing new_origin and current_origin. |
---|
| 616 | If you get both, do a convertion from the old to the new. |
---|
| 617 | |
---|
| 618 | If you only get new_origin, the points are absolute, |
---|
| 619 | convert to relative |
---|
| 620 | |
---|
| 621 | if you only get the current_origin the points are relative, store |
---|
| 622 | as relative. |
---|
| 623 | |
---|
| 624 | if you get no georefs create a new georef based on the minimums of |
---|
| 625 | points_utm. (Another option would be to default to absolute) |
---|
| 626 | |
---|
| 627 | Yes, and this is done in another part of the code. |
---|
| 628 | Probably geospatial. |
---|
| 629 | |
---|
| 630 | If you don't supply either geo_refs, then supply a zone. If not |
---|
| 631 | the default zone will be used. |
---|
| 632 | |
---|
| 633 | precon: |
---|
| 634 | header has been called. |
---|
| 635 | """ |
---|
| 636 | |
---|
| 637 | number_of_points = len(points_utm) |
---|
| 638 | volumes = num.array(volumes) |
---|
| 639 | points_utm = num.array(points_utm) |
---|
| 640 | |
---|
| 641 | # Given the two geo_refs and the points, do the stuff |
---|
| 642 | # described in the method header |
---|
| 643 | # if this is needed else where, pull out as a function |
---|
| 644 | points_georeference = ensure_geo_reference(points_georeference) |
---|
| 645 | new_origin = ensure_geo_reference(new_origin) |
---|
| 646 | if new_origin is None and points_georeference is not None: |
---|
| 647 | points = points_utm |
---|
| 648 | geo_ref = points_georeference |
---|
| 649 | else: |
---|
| 650 | if new_origin is None: |
---|
| 651 | new_origin = Geo_reference(zone, min(points_utm[:,0]), |
---|
| 652 | min(points_utm[:,1])) |
---|
| 653 | points = new_origin.change_points_geo_ref(points_utm, |
---|
| 654 | points_georeference) |
---|
| 655 | geo_ref = new_origin |
---|
| 656 | |
---|
| 657 | # At this stage I need a georef and points |
---|
| 658 | # the points are relative to the georef |
---|
| 659 | geo_ref.write_NetCDF(outfile) |
---|
| 660 | |
---|
| 661 | # This will put the geo ref in the middle |
---|
| 662 | #geo_ref = Geo_reference(refzone,(max(x)+min(x))/2.0,(max(x)+min(y))/2.) |
---|
| 663 | |
---|
| 664 | x = points[:,0] |
---|
| 665 | y = points[:,1] |
---|
| 666 | |
---|
| 667 | if verbose: |
---|
| 668 | log.critical('------------------------------------------------') |
---|
| 669 | log.critical('More Statistics:') |
---|
| 670 | log.critical(' Extent (/lon):') |
---|
| 671 | log.critical(' x in [%f, %f], len(lat) == %d' |
---|
| 672 | % (min(x), max(x), len(x))) |
---|
| 673 | log.critical(' y in [%f, %f], len(lon) == %d' |
---|
| 674 | % (min(y), max(y), len(y))) |
---|
| 675 | #log.critical(' z in [%f, %f], len(z) == %d' |
---|
| 676 | # % (min(elevation), max(elevation), len(elevation))) |
---|
| 677 | log.critical('geo_ref: %s' % str(geo_ref)) |
---|
| 678 | log.critical('------------------------------------------------') |
---|
| 679 | |
---|
| 680 | outfile.variables['x'][:] = points[:,0] #- geo_ref.get_xllcorner() |
---|
| 681 | outfile.variables['y'][:] = points[:,1] #- geo_ref.get_yllcorner() |
---|
| 682 | outfile.variables['volumes'][:] = volumes.astype(num.int32) #On Opteron 64 |
---|
| 683 | |
---|
| 684 | |
---|
| 685 | def store_static_quantities(self, |
---|
| 686 | outfile, |
---|
| 687 | sww_precision=num.float32, |
---|
| 688 | verbose=False, |
---|
| 689 | **quant): |
---|
| 690 | """ |
---|
| 691 | Write the static quantity info. |
---|
| 692 | |
---|
| 693 | **quant is extra keyword arguments passed in. These must be |
---|
| 694 | the numpy arrays to be stored in the sww file at each timestep. |
---|
| 695 | |
---|
| 696 | The argument sww_precision allows for storing as either |
---|
| 697 | * single precision (default): num.float32 |
---|
| 698 | * double precision: num.float64 or num.float |
---|
| 699 | |
---|
| 700 | Precondition: |
---|
| 701 | store_triangulation and |
---|
| 702 | store_header have been called. |
---|
| 703 | """ |
---|
| 704 | |
---|
| 705 | # The dictionary quant must contain numpy arrays for each name. |
---|
| 706 | # These will typically be quantities from Domain such as friction |
---|
| 707 | # |
---|
| 708 | # Arrays not listed in static_quantitiues will be ignored, silently. |
---|
| 709 | # |
---|
| 710 | # This method will also write the ranges for each quantity, |
---|
| 711 | # e.g. stage_range, xmomentum_range and ymomentum_range |
---|
| 712 | for q in self.static_quantities: |
---|
| 713 | if not quant.has_key(q): |
---|
| 714 | msg = 'Values for quantity %s was not specified in ' % q |
---|
| 715 | msg += 'store_quantities so they cannot be stored.' |
---|
| 716 | raise NewQuantity, msg |
---|
| 717 | else: |
---|
| 718 | q_values = ensure_numeric(quant[q]) |
---|
| 719 | |
---|
| 720 | x = q_values.astype(sww_precision) |
---|
| 721 | outfile.variables[q][:] = x |
---|
| 722 | |
---|
| 723 | # This populates the _range values |
---|
| 724 | outfile.variables[q + Write_sww.RANGE][0] = num.min(x) |
---|
| 725 | outfile.variables[q + Write_sww.RANGE][1] = num.max(x) |
---|
| 726 | |
---|
| 727 | # FIXME: Hack for backwards compatibility with old viewer |
---|
| 728 | #if 'elevation' in self.static_quantities: |
---|
| 729 | # outfile.variables['z'][:] = outfile.variables['elevation'][:] |
---|
| 730 | |
---|
| 731 | |
---|
| 732 | |
---|
| 733 | |
---|
| 734 | |
---|
| 735 | def store_quantities(self, |
---|
| 736 | outfile, |
---|
| 737 | sww_precision=num.float32, |
---|
| 738 | slice_index=None, |
---|
| 739 | time=None, |
---|
| 740 | verbose=False, |
---|
| 741 | **quant): |
---|
| 742 | """ |
---|
| 743 | Write the quantity info at each timestep. |
---|
| 744 | |
---|
| 745 | **quant is extra keyword arguments passed in. These must be |
---|
| 746 | the numpy arrays to be stored in the sww file at each timestep. |
---|
| 747 | |
---|
| 748 | if the time array is already been built, use the slice_index |
---|
| 749 | to specify the index. |
---|
| 750 | |
---|
| 751 | Otherwise, use time to increase the time dimension |
---|
| 752 | |
---|
| 753 | Maybe make this general, but the viewer assumes these quantities, |
---|
| 754 | so maybe we don't want it general - unless the viewer is general |
---|
| 755 | |
---|
| 756 | The argument sww_precision allows for storing as either |
---|
| 757 | * single precision (default): num.float32 |
---|
| 758 | * double precision: num.float64 or num.float |
---|
| 759 | |
---|
| 760 | Precondition: |
---|
| 761 | store_triangulation and |
---|
| 762 | store_header have been called. |
---|
| 763 | """ |
---|
| 764 | |
---|
| 765 | if time is not None: |
---|
| 766 | file_time = outfile.variables['time'] |
---|
| 767 | slice_index = len(file_time) |
---|
| 768 | file_time[slice_index] = time |
---|
| 769 | else: |
---|
| 770 | slice_index = int(slice_index) # Has to be cast in case it was numpy.int |
---|
| 771 | |
---|
| 772 | # Write the named dynamic quantities |
---|
| 773 | # The dictionary quant must contain numpy arrays for each name. |
---|
| 774 | # These will typically be the conserved quantities from Domain |
---|
| 775 | # (Typically stage, xmomentum, ymomentum). |
---|
| 776 | # |
---|
| 777 | # Arrays not listed in dynamic_quantitiues will be ignored, silently. |
---|
| 778 | # |
---|
| 779 | # This method will also write the ranges for each quantity, |
---|
| 780 | # e.g. stage_range, xmomentum_range and ymomentum_range |
---|
| 781 | for q in self.dynamic_quantities: |
---|
| 782 | if not quant.has_key(q): |
---|
| 783 | msg = 'Values for quantity %s was not specified in ' % q |
---|
| 784 | msg += 'store_quantities so they cannot be stored.' |
---|
| 785 | raise NewQuantity, msg |
---|
| 786 | else: |
---|
| 787 | q_values = ensure_numeric(quant[q]) |
---|
| 788 | |
---|
| 789 | x = q_values.astype(sww_precision) |
---|
| 790 | outfile.variables[q][slice_index] = x |
---|
| 791 | |
---|
| 792 | |
---|
| 793 | # This updates the _range values |
---|
| 794 | q_range = outfile.variables[q + Write_sww.RANGE][:] |
---|
| 795 | q_values_min = num.min(q_values) |
---|
| 796 | if q_values_min < q_range[0]: |
---|
| 797 | outfile.variables[q + Write_sww.RANGE][0] = q_values_min |
---|
| 798 | q_values_max = num.max(q_values) |
---|
| 799 | if q_values_max > q_range[1]: |
---|
| 800 | outfile.variables[q + Write_sww.RANGE][1] = q_values_max |
---|
| 801 | |
---|
| 802 | ## |
---|
| 803 | # @brief Print the quantities in the underlying file. |
---|
| 804 | # @param outfile UNUSED. |
---|
| 805 | def verbose_quantities(self, outfile): |
---|
| 806 | log.critical('------------------------------------------------') |
---|
| 807 | log.critical('More Statistics:') |
---|
| 808 | for q in self.dynamic_quantities: |
---|
| 809 | log.critical(' %s in [%f, %f]' |
---|
| 810 | % (q, outfile.variables[q+Write_sww.RANGE][0], |
---|
| 811 | outfile.variables[q+Write_sww.RANGE][1])) |
---|
| 812 | log.critical('------------------------------------------------') |
---|
| 813 | |
---|
[7767] | 814 | |
---|
| 815 | |
---|
| 816 | |
---|
| 817 | def extent_sww(file_name): |
---|
[7841] | 818 | """Read in an sww file, then get its extents |
---|
[7767] | 819 | |
---|
| 820 | Input: |
---|
| 821 | file_name - the sww file |
---|
| 822 | |
---|
| 823 | Output: |
---|
| 824 | A list: [min(x),max(x),min(y),max(y),min(stage.flat),max(stage.flat)] |
---|
| 825 | """ |
---|
| 826 | |
---|
| 827 | from Scientific.IO.NetCDF import NetCDFFile |
---|
| 828 | |
---|
| 829 | #Get NetCDF |
---|
| 830 | fid = NetCDFFile(file_name, netcdf_mode_r) |
---|
| 831 | |
---|
| 832 | # Get the variables |
---|
| 833 | x = fid.variables['x'][:] |
---|
| 834 | y = fid.variables['y'][:] |
---|
| 835 | stage = fid.variables['stage'][:] |
---|
| 836 | |
---|
| 837 | fid.close() |
---|
| 838 | |
---|
| 839 | return [min(x), max(x), min(y), max(y), num.min(stage), num.max(stage)] |
---|
| 840 | |
---|
| 841 | |
---|
| 842 | def load_sww_as_domain(filename, boundary=None, t=None, |
---|
| 843 | fail_if_NaN=True, NaN_filler=0, |
---|
| 844 | verbose=False, very_verbose=False): |
---|
| 845 | """ |
---|
[7841] | 846 | Load an sww file into a domain. |
---|
| 847 | |
---|
[7767] | 848 | Usage: domain = load_sww_as_domain('file.sww', |
---|
| 849 | t=time (default = last time in file)) |
---|
| 850 | |
---|
| 851 | Boundary is not recommended if domain.smooth is not selected, as it |
---|
| 852 | uses unique coordinates, but not unique boundaries. This means that |
---|
| 853 | the boundary file will not be compatable with the coordinates, and will |
---|
| 854 | give a different final boundary, or crash. |
---|
| 855 | """ |
---|
| 856 | |
---|
| 857 | from Scientific.IO.NetCDF import NetCDFFile |
---|
[7796] | 858 | from anuga.shallow_water.shallow_water_domain import Domain |
---|
[7767] | 859 | |
---|
| 860 | # initialise NaN. |
---|
| 861 | NaN = 9.969209968386869e+036 |
---|
| 862 | |
---|
| 863 | if verbose: log.critical('Reading from %s' % filename) |
---|
| 864 | |
---|
| 865 | fid = NetCDFFile(filename, netcdf_mode_r) # Open existing file for read |
---|
| 866 | time = fid.variables['time'] # Timesteps |
---|
| 867 | if t is None: |
---|
| 868 | t = time[-1] |
---|
| 869 | time_interp = get_time_interp(time,t) |
---|
| 870 | |
---|
| 871 | # Get the variables as numeric arrays |
---|
| 872 | x = fid.variables['x'][:] # x-coordinates of vertices |
---|
| 873 | y = fid.variables['y'][:] # y-coordinates of vertices |
---|
| 874 | elevation = fid.variables['elevation'] # Elevation |
---|
| 875 | stage = fid.variables['stage'] # Water level |
---|
| 876 | xmomentum = fid.variables['xmomentum'] # Momentum in the x-direction |
---|
| 877 | ymomentum = fid.variables['ymomentum'] # Momentum in the y-direction |
---|
| 878 | |
---|
| 879 | starttime = fid.starttime[0] |
---|
| 880 | volumes = fid.variables['volumes'][:] # Connectivity |
---|
| 881 | coordinates = num.transpose(num.asarray([x.tolist(), y.tolist()])) |
---|
| 882 | # FIXME (Ole): Something like this might be better: |
---|
| 883 | # concatenate((x, y), axis=1) |
---|
| 884 | # or concatenate((x[:,num.newaxis], x[:,num.newaxis]), axis=1) |
---|
| 885 | |
---|
| 886 | conserved_quantities = [] |
---|
| 887 | interpolated_quantities = {} |
---|
| 888 | other_quantities = [] |
---|
| 889 | |
---|
| 890 | # get geo_reference |
---|
| 891 | try: # sww files don't have to have a geo_ref |
---|
| 892 | geo_reference = Geo_reference(NetCDFObject=fid) |
---|
| 893 | except: # AttributeError, e: |
---|
| 894 | geo_reference = None |
---|
| 895 | |
---|
| 896 | if verbose: log.critical(' getting quantities') |
---|
| 897 | |
---|
| 898 | for quantity in fid.variables.keys(): |
---|
| 899 | dimensions = fid.variables[quantity].dimensions |
---|
| 900 | if 'number_of_timesteps' in dimensions: |
---|
| 901 | conserved_quantities.append(quantity) |
---|
| 902 | interpolated_quantities[quantity] = \ |
---|
| 903 | interpolated_quantity(fid.variables[quantity][:], time_interp) |
---|
| 904 | else: |
---|
| 905 | other_quantities.append(quantity) |
---|
| 906 | |
---|
| 907 | other_quantities.remove('x') |
---|
| 908 | other_quantities.remove('y') |
---|
| 909 | #other_quantities.remove('z') |
---|
| 910 | other_quantities.remove('volumes') |
---|
| 911 | try: |
---|
| 912 | other_quantities.remove('stage_range') |
---|
| 913 | other_quantities.remove('xmomentum_range') |
---|
| 914 | other_quantities.remove('ymomentum_range') |
---|
| 915 | other_quantities.remove('elevation_range') |
---|
| 916 | except: |
---|
| 917 | pass |
---|
| 918 | |
---|
| 919 | conserved_quantities.remove('time') |
---|
| 920 | |
---|
| 921 | if verbose: log.critical(' building domain') |
---|
| 922 | |
---|
| 923 | # From domain.Domain: |
---|
| 924 | # domain = Domain(coordinates, volumes,\ |
---|
| 925 | # conserved_quantities = conserved_quantities,\ |
---|
| 926 | # other_quantities = other_quantities,zone=zone,\ |
---|
| 927 | # xllcorner=xllcorner, yllcorner=yllcorner) |
---|
| 928 | |
---|
| 929 | # From shallow_water.Domain: |
---|
| 930 | coordinates = coordinates.tolist() |
---|
| 931 | volumes = volumes.tolist() |
---|
| 932 | # FIXME:should this be in mesh? (peter row) |
---|
| 933 | if fid.smoothing == 'Yes': |
---|
| 934 | unique = False |
---|
| 935 | else: |
---|
| 936 | unique = True |
---|
| 937 | if unique: |
---|
| 938 | coordinates, volumes, boundary = weed(coordinates, volumes,boundary) |
---|
| 939 | |
---|
| 940 | |
---|
| 941 | |
---|
| 942 | try: |
---|
| 943 | domain = Domain(coordinates, volumes, boundary) |
---|
| 944 | except AssertionError, e: |
---|
| 945 | fid.close() |
---|
| 946 | msg = 'Domain could not be created: %s. ' \ |
---|
| 947 | 'Perhaps use "fail_if_NaN=False and NaN_filler = ..."' % e |
---|
| 948 | raise DataDomainError, msg |
---|
| 949 | |
---|
| 950 | if not boundary is None: |
---|
| 951 | domain.boundary = boundary |
---|
| 952 | |
---|
| 953 | domain.geo_reference = geo_reference |
---|
| 954 | |
---|
| 955 | domain.starttime = float(starttime) + float(t) |
---|
| 956 | domain.time = 0.0 |
---|
| 957 | |
---|
| 958 | for quantity in other_quantities: |
---|
| 959 | try: |
---|
| 960 | NaN = fid.variables[quantity].missing_value |
---|
| 961 | except: |
---|
| 962 | pass # quantity has no missing_value number |
---|
| 963 | X = fid.variables[quantity][:] |
---|
| 964 | if very_verbose: |
---|
| 965 | log.critical(' %s' % str(quantity)) |
---|
| 966 | log.critical(' NaN = %s' % str(NaN)) |
---|
| 967 | log.critical(' max(X)') |
---|
| 968 | log.critical(' %s' % str(max(X))) |
---|
| 969 | log.critical(' max(X)==NaN') |
---|
| 970 | log.critical(' %s' % str(max(X)==NaN)) |
---|
| 971 | log.critical('') |
---|
| 972 | if max(X) == NaN or min(X) == NaN: |
---|
| 973 | if fail_if_NaN: |
---|
| 974 | msg = 'quantity "%s" contains no_data entry' % quantity |
---|
| 975 | raise DataMissingValuesError, msg |
---|
| 976 | else: |
---|
| 977 | data = (X != NaN) |
---|
| 978 | X = (X*data) + (data==0)*NaN_filler |
---|
| 979 | if unique: |
---|
| 980 | X = num.resize(X, (len(X)/3, 3)) |
---|
| 981 | domain.set_quantity(quantity, X) |
---|
| 982 | # |
---|
| 983 | for quantity in conserved_quantities: |
---|
| 984 | try: |
---|
| 985 | NaN = fid.variables[quantity].missing_value |
---|
| 986 | except: |
---|
| 987 | pass # quantity has no missing_value number |
---|
| 988 | X = interpolated_quantities[quantity] |
---|
| 989 | if very_verbose: |
---|
| 990 | log.critical(' %s' % str(quantity)) |
---|
| 991 | log.critical(' NaN = %s' % str(NaN)) |
---|
| 992 | log.critical(' max(X)') |
---|
| 993 | log.critical(' %s' % str(max(X))) |
---|
| 994 | log.critical(' max(X)==NaN') |
---|
| 995 | log.critical(' %s' % str(max(X)==NaN)) |
---|
| 996 | log.critical('') |
---|
| 997 | if max(X) == NaN or min(X) == NaN: |
---|
| 998 | if fail_if_NaN: |
---|
| 999 | msg = 'quantity "%s" contains no_data entry' % quantity |
---|
| 1000 | raise DataMissingValuesError, msg |
---|
| 1001 | else: |
---|
| 1002 | data = (X != NaN) |
---|
| 1003 | X = (X*data) + (data==0)*NaN_filler |
---|
| 1004 | if unique: |
---|
| 1005 | X = num.resize(X, (X.shape[0]/3, 3)) |
---|
| 1006 | domain.set_quantity(quantity, X) |
---|
| 1007 | |
---|
| 1008 | fid.close() |
---|
| 1009 | |
---|
| 1010 | return domain |
---|
| 1011 | |
---|
| 1012 | |
---|
[7770] | 1013 | def get_mesh_and_quantities_from_file(filename, |
---|
| 1014 | quantities=None, |
---|
| 1015 | verbose=False): |
---|
| 1016 | """Get and rebuild mesh structure and associated quantities from sww file |
---|
| 1017 | |
---|
| 1018 | Input: |
---|
| 1019 | filename - Name os sww file |
---|
| 1020 | quantities - Names of quantities to load |
---|
| 1021 | |
---|
| 1022 | Output: |
---|
| 1023 | mesh - instance of class Interpolate |
---|
| 1024 | (including mesh and interpolation functionality) |
---|
| 1025 | quantities - arrays with quantity values at each mesh node |
---|
| 1026 | time - vector of stored timesteps |
---|
| 1027 | |
---|
| 1028 | This function is used by e.g.: |
---|
| 1029 | get_interpolated_quantities_at_polyline_midpoints |
---|
| 1030 | """ |
---|
| 1031 | |
---|
| 1032 | # FIXME (Ole): Maybe refactor filefunction using this more fundamental code. |
---|
| 1033 | |
---|
| 1034 | import types |
---|
| 1035 | from Scientific.IO.NetCDF import NetCDFFile |
---|
| 1036 | from anuga.abstract_2d_finite_volumes.neighbour_mesh import Mesh |
---|
| 1037 | |
---|
| 1038 | if verbose: log.critical('Reading from %s' % filename) |
---|
| 1039 | |
---|
| 1040 | fid = NetCDFFile(filename, netcdf_mode_r) # Open existing file for read |
---|
| 1041 | time = fid.variables['time'][:] # Time vector |
---|
| 1042 | time += fid.starttime[0] |
---|
| 1043 | |
---|
| 1044 | # Get the variables as numeric arrays |
---|
| 1045 | x = fid.variables['x'][:] # x-coordinates of nodes |
---|
| 1046 | y = fid.variables['y'][:] # y-coordinates of nodes |
---|
| 1047 | elevation = fid.variables['elevation'][:] # Elevation |
---|
| 1048 | stage = fid.variables['stage'][:] # Water level |
---|
| 1049 | xmomentum = fid.variables['xmomentum'][:] # Momentum in the x-direction |
---|
| 1050 | ymomentum = fid.variables['ymomentum'][:] # Momentum in the y-direction |
---|
| 1051 | |
---|
| 1052 | # Mesh (nodes (Mx2), triangles (Nx3)) |
---|
| 1053 | nodes = num.concatenate((x[:,num.newaxis], y[:,num.newaxis]), axis=1) |
---|
| 1054 | triangles = fid.variables['volumes'][:] |
---|
| 1055 | |
---|
| 1056 | # Get geo_reference |
---|
| 1057 | try: |
---|
| 1058 | geo_reference = Geo_reference(NetCDFObject=fid) |
---|
| 1059 | except: #AttributeError, e: |
---|
| 1060 | # Sww files don't have to have a geo_ref |
---|
| 1061 | geo_reference = None |
---|
| 1062 | |
---|
| 1063 | if verbose: log.critical(' building mesh from sww file %s' % filename) |
---|
| 1064 | |
---|
| 1065 | boundary = None |
---|
| 1066 | |
---|
| 1067 | #FIXME (Peter Row): Should this be in mesh? |
---|
| 1068 | if fid.smoothing != 'Yes': |
---|
| 1069 | nodes = nodes.tolist() |
---|
| 1070 | triangles = triangles.tolist() |
---|
| 1071 | nodes, triangles, boundary = weed(nodes, triangles, boundary) |
---|
| 1072 | |
---|
| 1073 | try: |
---|
| 1074 | mesh = Mesh(nodes, triangles, boundary, geo_reference=geo_reference) |
---|
| 1075 | except AssertionError, e: |
---|
| 1076 | fid.close() |
---|
| 1077 | msg = 'Domain could not be created: %s. "' % e |
---|
| 1078 | raise DataDomainError, msg |
---|
| 1079 | |
---|
| 1080 | quantities = {} |
---|
| 1081 | quantities['elevation'] = elevation |
---|
| 1082 | quantities['stage'] = stage |
---|
| 1083 | quantities['xmomentum'] = xmomentum |
---|
| 1084 | quantities['ymomentum'] = ymomentum |
---|
| 1085 | |
---|
| 1086 | fid.close() |
---|
| 1087 | |
---|
| 1088 | return mesh, quantities, time |
---|
| 1089 | |
---|
| 1090 | |
---|
[7767] | 1091 | def get_time_interp(time, t=None): |
---|
[7841] | 1092 | """Finds the ratio and index for time interpolation. |
---|
| 1093 | time is an array of time steps |
---|
| 1094 | t is the sample time. |
---|
| 1095 | returns a tuple containing index into time, and ratio |
---|
| 1096 | """ |
---|
[7767] | 1097 | if t is None: |
---|
| 1098 | t=time[-1] |
---|
| 1099 | index = -1 |
---|
| 1100 | ratio = 0. |
---|
| 1101 | else: |
---|
| 1102 | T = time |
---|
| 1103 | tau = t |
---|
| 1104 | index=0 |
---|
| 1105 | msg = 'Time interval derived from file %s [%s:%s]' \ |
---|
| 1106 | % ('FIXMEfilename', T[0], T[-1]) |
---|
| 1107 | msg += ' does not match model time: %s' % tau |
---|
| 1108 | if tau < time[0]: raise DataTimeError, msg |
---|
| 1109 | if tau > time[-1]: raise DataTimeError, msg |
---|
| 1110 | while tau > time[index]: index += 1 |
---|
| 1111 | while tau < time[index]: index -= 1 |
---|
| 1112 | if tau == time[index]: |
---|
| 1113 | #Protect against case where tau == time[-1] (last time) |
---|
| 1114 | # - also works in general when tau == time[i] |
---|
| 1115 | ratio = 0 |
---|
| 1116 | else: |
---|
| 1117 | #t is now between index and index+1 |
---|
| 1118 | ratio = (tau - time[index])/(time[index+1] - time[index]) |
---|
| 1119 | |
---|
| 1120 | return (index, ratio) |
---|
| 1121 | |
---|
| 1122 | |
---|
| 1123 | |
---|
| 1124 | ## |
---|
| 1125 | # @brief Interpolate a quantity wrt time. |
---|
| 1126 | # @param saved_quantity The quantity to interpolate. |
---|
| 1127 | # @param time_interp (index, ratio) |
---|
| 1128 | # @return A vector of interpolated values. |
---|
| 1129 | def interpolated_quantity(saved_quantity, time_interp): |
---|
| 1130 | '''Given an index and ratio, interpolate quantity with respect to time.''' |
---|
| 1131 | |
---|
| 1132 | index, ratio = time_interp |
---|
| 1133 | |
---|
| 1134 | Q = saved_quantity |
---|
| 1135 | |
---|
| 1136 | if ratio > 0: |
---|
| 1137 | q = (1-ratio)*Q[index] + ratio*Q[index+1] |
---|
| 1138 | else: |
---|
| 1139 | q = Q[index] |
---|
| 1140 | |
---|
| 1141 | #Return vector of interpolated values |
---|
| 1142 | return q |
---|
| 1143 | |
---|
| 1144 | |
---|
| 1145 | def weed(coordinates, volumes, boundary=None): |
---|
[7841] | 1146 | """ Excise all duplicate points. |
---|
| 1147 | """ |
---|
[7767] | 1148 | if isinstance(coordinates, num.ndarray): |
---|
| 1149 | coordinates = coordinates.tolist() |
---|
| 1150 | if isinstance(volumes, num.ndarray): |
---|
| 1151 | volumes = volumes.tolist() |
---|
| 1152 | |
---|
| 1153 | unique = False |
---|
| 1154 | point_dict = {} |
---|
| 1155 | same_point = {} |
---|
| 1156 | for i in range(len(coordinates)): |
---|
| 1157 | point = tuple(coordinates[i]) |
---|
| 1158 | if point_dict.has_key(point): |
---|
| 1159 | unique = True |
---|
| 1160 | same_point[i] = point |
---|
| 1161 | #to change all point i references to point j |
---|
| 1162 | else: |
---|
| 1163 | point_dict[point] = i |
---|
| 1164 | same_point[i] = point |
---|
| 1165 | |
---|
| 1166 | coordinates = [] |
---|
| 1167 | i = 0 |
---|
| 1168 | for point in point_dict.keys(): |
---|
| 1169 | point = tuple(point) |
---|
| 1170 | coordinates.append(list(point)) |
---|
| 1171 | point_dict[point] = i |
---|
| 1172 | i += 1 |
---|
| 1173 | |
---|
| 1174 | for volume in volumes: |
---|
| 1175 | for i in range(len(volume)): |
---|
| 1176 | index = volume[i] |
---|
| 1177 | if index > -1: |
---|
| 1178 | volume[i] = point_dict[same_point[index]] |
---|
| 1179 | |
---|
| 1180 | new_boundary = {} |
---|
| 1181 | if not boundary is None: |
---|
| 1182 | for segment in boundary.keys(): |
---|
| 1183 | point0 = point_dict[same_point[segment[0]]] |
---|
| 1184 | point1 = point_dict[same_point[segment[1]]] |
---|
| 1185 | label = boundary[segment] |
---|
| 1186 | #FIXME should the bounday attributes be concaterated |
---|
| 1187 | #('exterior, pond') or replaced ('pond')(peter row) |
---|
| 1188 | |
---|
| 1189 | if new_boundary.has_key((point0, point1)): |
---|
| 1190 | new_boundary[(point0,point1)] = new_boundary[(point0, point1)] |
---|
| 1191 | |
---|
| 1192 | elif new_boundary.has_key((point1, point0)): |
---|
| 1193 | new_boundary[(point1,point0)] = new_boundary[(point1, point0)] |
---|
| 1194 | else: new_boundary[(point0, point1)] = label |
---|
| 1195 | |
---|
| 1196 | boundary = new_boundary |
---|
| 1197 | |
---|
| 1198 | return coordinates, volumes, boundary |
---|
[7770] | 1199 | |
---|
| 1200 | |
---|
| 1201 | |
---|